Elbow Plot for Clustering

Heatmap

Number of Genes

Cluster Enrichments

Ectoderm Cluster

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

GO_Biological_Process_2018

KEGG_2019

Neuroectoderm Cluster

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

GO_Biological_Process_2018

KEGG_2019

Mesoderm Cluster

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

GO_Biological_Process_2018

KEGG_2019

Overlap between targets downregulated in WT vs. LOF and all clusters

Venn Diagram

Upset Plot

Resampling

Mesoderm

n
## [1] 50000
sum(res > 739)/n
## [1] 0

Neuroectoderm

n
## [1] 50000
sum(res > 292)/n
## [1] 0

Ectoderm

n
## [1] 50000
sum(res > 161)/n
## [1] 1

Overlap Enrichments

Downregulated & Neuroectoderm Overlap

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

Downregulated & Mesoderm Overlap

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

Mesoderm only

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

Neuroectoderm only

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

Downregulated only

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

Overlap between targets UPREGULATED in WT vs. LOF and all clusters

Venn Diagram

Upset Plot

Resampling

Mesoderm

n
## [1] 50000
sum(res > 223)/n
## [1] 1

Neuroectoderm

n
## [1] 50000
sum(res > 109)/n
## [1] 0.99942

Ectoderm

n
## [1] 50000
sum(res > 629)/n
## [1] 0

Overlap Enrichments

Upregulated & Ectoderm Overlap

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

Ectoderm only

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

Upregulated only

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

Combined Upset Plot

Session Info

## R version 4.0.5 (2021-03-31)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
##  [1] grid      parallel  stats4    stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] png_0.1-7                             UpSetR_1.4.0                         
##  [3] enrichR_3.0                           VennDiagram_1.6.20                   
##  [5] futile.logger_1.4.3                   org.Dm.eg.db_3.12.0                  
##  [7] msigdbr_7.2.1                         cowplot_1.1.1                        
##  [9] ggpubr_0.4.0                          data.table_1.14.0                    
## [11] DT_0.17                               forcats_0.5.1                        
## [13] dplyr_1.0.5                           purrr_0.3.4                          
## [15] readr_1.4.0                           tidyr_1.1.3                          
## [17] tibble_3.1.0                          tidyverse_1.3.0                      
## [19] factoextra_1.0.7                      ggplot2_3.3.3                        
## [21] cluster_2.1.1                         stringr_1.4.0                        
## [23] enrichplot_1.13.0                     ReactomePA_1.34.0                    
## [25] clusterProfiler_3.18.1                BSgenome.Dmelanogaster.UCSC.dm6_1.4.1
## [27] BSgenome_1.58.0                       rtracklayer_1.50.0                   
## [29] Biostrings_2.58.0                     XVector_0.30.0                       
## [31] pheatmap_1.0.12                       geneplotter_1.68.0                   
## [33] annotate_1.68.0                       XML_3.99-0.6                         
## [35] reshape_0.8.8                         lattice_0.20-41                      
## [37] gridExtra_2.3                         RColorBrewer_1.1-2                   
## [39] GenomicFeatures_1.42.3                AnnotationDbi_1.52.0                 
## [41] knitr_1.31                            DESeq2_1.30.1                        
## [43] SummarizedExperiment_1.20.0           Biobase_2.50.0                       
## [45] MatrixGenerics_1.2.1                  matrixStats_0.58.0                   
## [47] GenomicRanges_1.42.0                  GenomeInfoDb_1.26.7                  
## [49] IRanges_2.24.1                        S4Vectors_0.28.1                     
## [51] BiocGenerics_0.36.0                  
## 
## loaded via a namespace (and not attached):
##   [1] utf8_1.2.1               tidyselect_1.1.0         RSQLite_2.2.6           
##   [4] htmlwidgets_1.5.3        BiocParallel_1.24.1      scatterpie_0.1.5        
##   [7] munsell_0.5.0            withr_2.4.1              colorspace_2.0-0        
##  [10] GOSemSim_2.16.1          highr_0.8                rstudioapi_0.13         
##  [13] ggsignif_0.6.1           DOSE_3.16.0              labeling_0.4.2          
##  [16] GenomeInfoDbData_1.2.4   polyclip_1.10-0          bit64_4.0.5             
##  [19] farver_2.1.0             rprojroot_2.0.2          downloader_0.4          
##  [22] vctrs_0.3.7              treeio_1.14.4            generics_0.1.0          
##  [25] lambda.r_1.2.4           xfun_0.22                BiocFileCache_1.14.0    
##  [28] R6_2.5.0                 graphlayouts_0.7.1       locfit_1.5-9.4          
##  [31] bitops_1.0-6             cachem_1.0.4             fgsea_1.16.0            
##  [34] DelayedArray_0.16.3      assertthat_0.2.1         scales_1.1.1            
##  [37] ggraph_2.0.5             gtable_0.3.0             tidygraph_1.2.0         
##  [40] rlang_0.4.10             genefilter_1.72.1        splines_4.0.5           
##  [43] rstatix_0.7.0            lazyeval_0.2.2           broom_0.7.6             
##  [46] checkmate_2.0.0          abind_1.4-5              BiocManager_1.30.12     
##  [49] yaml_2.2.1               reshape2_1.4.4           modelr_0.1.8            
##  [52] crosstalk_1.1.1          backports_1.2.1          qvalue_2.22.0           
##  [55] tools_4.0.5              ellipsis_0.3.1           jquerylib_0.1.3         
##  [58] Rcpp_1.0.6               plyr_1.8.6               progress_1.2.2          
##  [61] zlibbioc_1.36.0          RCurl_1.98-1.3           prettyunits_1.1.1       
##  [64] openssl_1.4.3            viridis_0.5.1            haven_2.3.1             
##  [67] ggrepel_0.9.1            fs_1.5.0                 magrittr_2.0.1          
##  [70] futile.options_1.0.1     openxlsx_4.2.3           DO.db_2.9               
##  [73] reprex_2.0.0             reactome.db_1.74.0       hms_1.0.0               
##  [76] patchwork_1.1.1          evaluate_0.14            xtable_1.8-4            
##  [79] rio_0.5.26               readxl_1.3.1             compiler_4.0.5          
##  [82] biomaRt_2.46.3           crayon_1.4.1             shadowtext_0.0.7        
##  [85] htmltools_0.5.1.1        aplot_0.0.6              lubridate_1.7.10        
##  [88] DBI_1.1.1                formatR_1.8              tweenr_1.0.2            
##  [91] dbplyr_2.1.1             MASS_7.3-53.1            rappdirs_0.3.3          
##  [94] car_3.0-10               Matrix_1.3-2             cli_2.4.0               
##  [97] igraph_1.2.6             pkgconfig_2.0.3          rvcheck_0.1.8           
## [100] GenomicAlignments_1.26.0 foreign_0.8-81           xml2_1.3.2              
## [103] ggtree_2.4.2             bslib_0.2.4              rvest_1.0.0             
## [106] digest_0.6.27            graph_1.68.0             rmarkdown_2.7           
## [109] cellranger_1.1.0         fastmatch_1.1-0          tidytree_0.3.4          
## [112] curl_4.3                 Rsamtools_2.6.0          graphite_1.36.0         
## [115] rjson_0.2.20             lifecycle_1.0.0          nlme_3.1-152            
## [118] jsonlite_1.7.2           carData_3.0-4            viridisLite_0.4.0       
## [121] askpass_1.1              fansi_0.4.2              pillar_1.6.0            
## [124] fastmap_1.1.0            httr_1.4.2               survival_3.2-10         
## [127] GO.db_3.12.1             glue_1.4.2               zip_2.1.1               
## [130] bit_4.0.4                ggforce_0.3.3            stringi_1.5.3           
## [133] sass_0.3.1               blob_1.2.1               memoise_2.0.0           
## [136] ape_5.5